Wastewater-based epidemiology (WBE) has been proven to be beneficial in predicting the spread of COVID-19 in communities across the world since the start of the pandemic. It has become of increasing concern to track the evolution of the virus as new variants may pose higher risks of infectivity or alter its interactions with the host immune system. The current focus of the genetic sequencing of SARS-CoV-2 on tracking variants is to use clinical data collected from nasopharyngeal swabs of infected individuals. However, the sequencing of wastewater samples is promising to provide a more comprehensive understanding of the genetic diversity in the community. Previous study has reported that ultrafiltration-based method can concentrate virus particles with minimum damage to viral genome and thus benefiting high genome sequence coverage. However, the high costs of ultrafilter membranes prevent wide application for processing wastewater. Here, we demonstrate the utilization of reusable tangential flow filtration method for processing wastewater and achieve nearly full genome sequencing of SARS-CoV-2 from wastewater. This method involves membrane washing step between runs, which effectively remove remaining nucleic acids of SARS-CoV-2 and allow multiple-time use of the same membrane. We will also present the bioinformatic pipelines that we develop to analyze SARS-CoV-2 variants based on the whole-genome sequencing data. Our results provide a cost-effective wastewater processing method for the intention of genetic sequencing which can aid in future WBE efforts to track the spread of viral lineages.

Whole-genome sequencing of SARS-CoV-2 in wastewater using reusable ultrafiltration method

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ACS Fall 2022

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